Obsidian

Obsidian is a note-taking app over a folder of Markdown files on your own machine. That storage decision is the whole argument: your notes are readable without Obsidian, greppable by other tools, and not subject to a service shutting down or changing terms. Backlinks and the graph view make the cross-referencing worthwhile at scale, and the plugin ecosystem covers most workflow gaps. It pairs naturally with local models — a vault of plain files is exactly the input a local AI pipeline wants.